Usually not. With Portfolio diversity and Avoid Duplicates Across Groups turned off, SaberSim solves your whole portfolio at once, and order has no effect.
Order only matters when SaberSim has to solve groups one at a time, which happens in two cases.
Avoid Duplicates Across Groups is on. To keep the same lineup out of two groups, SaberSim has to know what the first group took before it fills the second, so groups are solved top to bottom and the ones higher up get first pick. The default sort is $/entry, highest first, so your most expensive entries pick first. Drag a group up to give it an earlier pick.
A group uses Uniques instead of Portfolio. Min Uniques is enforced lineup by lineup, so SaberSim fills each entry in order and the order decides which lineup each one gets.
If neither applies, arrange groups however you like. Reordering reruns the diversifier either way.